t/SeqFeature/Location.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use Bio::Root::Test;
   8
   9     test_begin(-tests => 109);
  10
  11     use_ok('Bio::Location::Simple');
  12     use_ok('Bio::Location::Split');
  13     use_ok('Bio::Location::Fuzzy');
  14     use_ok('Bio::SeqFeature::Generic');
  15     use_ok('Bio::SeqFeature::SimilarityPair');
  16     use_ok('Bio::SeqFeature::FeaturePair');
  17     use_ok('Bio::SeqFeature::Lite');
  18 }
  19
  20 my $simple = Bio::Location::Simple->new('-start' => 10, '-end' => 20,
  21                                        '-strand' => 1, -seq_id => 'my1');
  22 isa_ok($simple, 'Bio::LocationI');
  23 isa_ok($simple, 'Bio::RangeI');
  24
  25 is($simple->start, 10, 'Bio::Location::Simple tests');
  26 is($simple->end, 20);
  27 is($simple->seq_id, 'my1');
  28
  29 my ($loc) = $simple->each_Location();
  30 ok($loc);
  31 is("$loc", "$simple");
  32
  33 my $generic = Bio::SeqFeature::Generic->new('-start' => 5, '-end' => 30,
  34                                            '-strand' => 1);
  35
  36 isa_ok($generic,'Bio::SeqFeatureI', 'Bio::SeqFeature::Generic' );
  37 isa_ok($generic,'Bio::RangeI');
  38 is($generic->start, 5);
  39 is($generic->end, 30);
  40
  41 my $lite_pos  = Bio::SeqFeature::Lite->new(-start => 1000, -stop => 2000, -strand => '+');
  42 my $lite_neg  = Bio::SeqFeature::Lite->new(-start => 1000, -end  => 2000, -strand => '-');
  43 my $lite_none = Bio::SeqFeature::Lite->new(-start => 1000, -stop => 2000, -strand => '.');
  44 is($lite_pos->strand,  1);
  45 is($lite_neg->strand, -1);
  46 is($lite_neg->end,  2000);
  47 is($lite_neg->stop, 2000);
  48 is($lite_none->strand, 0);
  49
  50 my $similarity = Bio::SeqFeature::SimilarityPair->new();
  51
  52 my $feat1 = Bio::SeqFeature::Generic->new('-start' => 30, '-end' => 43,
  53                                          '-strand' => -1);
  54 my $feat2 = Bio::SeqFeature::Generic->new('-start' => 80, '-end' => 90,
  55                                          '-strand' => -1);
  56
  57 my $featpair = Bio::SeqFeature::FeaturePair->new('-feature1' => $feat1,
  58                                                 '-feature2' => $feat2 );
  59
  60 my $feat3 = Bio::SeqFeature::Generic->new('-start' => 35, '-end' => 50,
  61                                          '-strand' => -1);
  62
  63 is($featpair->start, 30,'Bio::SeqFeature::FeaturePair tests');
  64 is($featpair->end,  43);
  65
  66 is($featpair->length, 14);
  67
  68 ok($featpair->overlaps($feat3));
  69 ok($generic->overlaps($simple), 'Bio::SeqFeature::Generic tests');
  70 ok($generic->contains($simple));
  71
  72 # fuzzy location tests
  73 my $fuzzy = Bio::Location::Fuzzy->new('-start'  =>'<10',
  74                                      '-end'    => 20,
  75                                      -strand   =>1,
  76                                      -seq_id   =>'my2');
  77
  78 is($fuzzy->strand, 1, 'Bio::Location::Fuzzy tests');
  79 is($fuzzy->start, 10);
  80 is($fuzzy->end,20);
  81 ok(!defined $fuzzy->min_start);
  82 is($fuzzy->max_start, 10);
  83 is($fuzzy->min_end, 20);
  84 is($fuzzy->max_end, 20);
  85 is($fuzzy->location_type, 'EXACT');
  86 is($fuzzy->start_pos_type, 'BEFORE');
  87 is($fuzzy->end_pos_type, 'EXACT');
  88 is($fuzzy->seq_id, 'my2');
  89 is($fuzzy->seq_id('my3'), 'my3');
  90
  91 ($loc) = $fuzzy->each_Location();
  92 ok($loc);
  93 is("$loc", "$fuzzy");
  94
  95 # split location tests
  96 my $splitlocation = Bio::Location::Split->new();
  97 my $f = Bio::Location::Simple->new(-start  => 13,
  98                                   -end    => 30,
  99                                   -strand => 1);
 100 $splitlocation->add_sub_Location($f);
 101 is($f->start, 13, 'Bio::Location::Split tests');
 102 is($f->min_start, 13);
 103 is($f->max_start,13);
 104
 105
 106 $f = Bio::Location::Simple->new(-start  =>30,
 107                                -end    =>90,
 108                                -strand =>1);
 109 $splitlocation->add_sub_Location($f);
 110
 111 $f = Bio::Location::Simple->new(-start  =>11,
 112                                -end    =>22,
 113                                -strand =>1);
 114 $splitlocation->add_sub_Location($f);
 115
 116 $f = Bio::Location::Simple->new(-start  =>19,
 117                                -end    =>20,
 118                                -strand =>1);
 119
 120 $splitlocation->add_sub_Location($f);
 121
 122 $f = Bio::Location::Fuzzy->new(-start  =>"<50",
 123                               -end    =>61,
 124                               -strand =>1);
 125 is($f->start, 50);
 126 ok(! defined $f->min_start);
 127 is($f->max_start, 50);
 128
 129 is(scalar($splitlocation->each_Location()), 4);
 130
 131 $splitlocation->add_sub_Location($f);
 132
 133 # For unsorted split locations like this:
 134 # ('join(13..30,30..90,11..22,19..20,<50..61)'),
 135 # BioPerl will assume Start and End belongs to the
 136 # first and last segments respectively, because sorting
 137 # would break real cases like circular cut by origin features
 138 is($splitlocation->end, 61);
 139 is($splitlocation->start, 13);
 140 is($splitlocation->sub_Location(),5);
 141 # Minimum Start and Maximum End in unsorted sublocations can be
 142 # achieved by asking explicitly sub_Location to sort the segments
 143 my @increase_sort_sublocs = $splitlocation->sub_Location(1);  # Forward sort by Start
 144 my @decrease_sort_sublocs = $splitlocation->sub_Location(-1); # Reverse sort by End
 145 is($increase_sort_sublocs[0]->min_start, 11);
 146 is($decrease_sort_sublocs[0]->max_end,   90);
 147
 148 is($fuzzy->to_FTstring(), '<10..20');
 149 $fuzzy->strand(-1);
 150 is($fuzzy->to_FTstring(), 'complement(<10..20)');
 151 is($simple->to_FTstring(), '10..20');
 152 $simple->strand(-1);
 153 is($simple->to_FTstring(), 'complement(10..20)');
 154 is( $splitlocation->to_FTstring(),
 155     'join(13..30,30..90,11..22,19..20,<50..61)');
 156
 157 # test for bug #1074
 158 $f = Bio::Location::Simple->new(-start  => 5,
 159                                -end    => 12,
 160                                -strand => -1);
 161 $splitlocation->add_sub_Location($f);
 162 is( $splitlocation->to_FTstring(),
 163     'join(13..30,30..90,11..22,19..20,<50..61,complement(5..12))',
 164         'Bugfix 1074');
 165 $splitlocation->strand(-1);
 166 is( $splitlocation->to_FTstring(),
 167     'complement(join(13..30,30..90,11..22,19..20,<50..61,5..12))');
 168
 169 $f = Bio::Location::Fuzzy->new(-start => '45.60',
 170                               -end   => '75^80');
 171
 172 is($f->to_FTstring(), '(45.60)..(75^80)');
 173 $f->start('20>');
 174 is($f->to_FTstring(), '>20..(75^80)');
 175
 176 # test that even when end < start that length is always positive
 177
 178 $f = Bio::Location::Simple->new(-verbose => -1,
 179                                -start   => 100,
 180                                -end     => 20,
 181                                -strand  => 1);
 182
 183 is($f->length, 81, 'Positive length');
 184 is($f->strand,-1);
 185
 186 # test that can call seq_id() on a split location;
 187 $splitlocation = Bio::Location::Split->new(-seq_id => 'mysplit1');
 188 is($splitlocation->seq_id,'mysplit1', 'seq_id() on Bio::Location::Split');
 189 is($splitlocation->seq_id('mysplit2'),'mysplit2');
 190
 191
 192 # Test Bio::Location::Exact
 193
 194 ok(my $exact = Bio::Location::Simple->new(-start    => 10,
 195                                          -end      => 20,
 196                                          -strand   => 1,
 197                                          -seq_id   => 'my1'));
 198 isa_ok($exact, 'Bio::LocationI');
 199 isa_ok($exact, 'Bio::RangeI');
 200
 201 is( $exact->start, 10, 'Bio::Location::Simple EXACT');
 202 is( $exact->end, 20);
 203 is( $exact->seq_id, 'my1');
 204 is( $exact->length, 11);
 205 is( $exact->location_type, 'EXACT');
 206
 207 ok ($exact = Bio::Location::Simple->new(-start         => 10,
 208                                       -end           => 11,
 209                                       -location_type => 'IN-BETWEEN',
 210                                       -strand        => 1,
 211                                       -seq_id        => 'my2'));
 212
 213 is($exact->start, 10, 'Bio::Location::Simple IN-BETWEEN');
 214 is($exact->end, 11);
 215 is($exact->seq_id, 'my2');
 216 is($exact->length, 0);
 217 is($exact->location_type, 'IN-BETWEEN');
 218
 219 eval {
 220     $exact = Bio::Location::Simple->new(-start         => 10,
 221                                        -end           => 12,
 222                                        -location_type => 'IN-BETWEEN');
 223 };
 224 ok( $@, 'Testing error handling' );
 225
 226 # testing error when assigning 10^11 simple location into fuzzy
 227 eval {
 228     ok $fuzzy = Bio::Location::Fuzzy->new(-start         => 10,
 229                                          -end           => 11,
 230                                          -location_type => '^',
 231                                          -strand        => 1,
 232                                          -seq_id        => 'my2');
 233 };
 234 ok( $@ );
 235
 236 $fuzzy = Bio::Location::Fuzzy->new(-location_type => '^',
 237                                   -strand        => 1,
 238                                   -seq_id        => 'my2');
 239
 240 $fuzzy->start(10);
 241 eval { $fuzzy->end(11) };
 242 ok($@);
 243
 244 $fuzzy = Bio::Location::Fuzzy->new(-location_type => '^',
 245                                   -strand        => 1,
 246                                   -seq_id        =>'my2');
 247
 248 $fuzzy->end(11);
 249 eval {
 250     $fuzzy->start(10);
 251 };
 252 ok($@);
 253
 254 # testing coodinate policy modules
 255
 256 use_ok('Bio::Location::WidestCoordPolicy');
 257 use_ok('Bio::Location::NarrowestCoordPolicy');
 258 use_ok('Bio::Location::AvWithinCoordPolicy');
 259
 260 $f = Bio::Location::Fuzzy->new(-start => '40.60',
 261                               -end   => '80.100');
 262 is $f->start, 40, 'Default coodinate policy';
 263 is $f->end, 100;
 264 is $f->length, 61;
 265 is $f->to_FTstring, '(40.60)..(80.100)';
 266 isa_ok($f->coordinate_policy, 'Bio::Location::WidestCoordPolicy');
 267
 268 # this gives an odd location string; is it legal?
 269 $f->coordinate_policy(Bio::Location::NarrowestCoordPolicy->new());
 270 is $f->start, 60, 'Narrowest coodinate policy';
 271 is $f->end, 80;
 272 is $f->length, 21;
 273 is $f->to_FTstring, '(60.60)..(80.80)';
 274 isa_ok($f->coordinate_policy, 'Bio::Location::NarrowestCoordPolicy');
 275
 276 # this gives an odd location string
 277 $f->coordinate_policy(Bio::Location::AvWithinCoordPolicy->new());
 278 is $f->start, 50, 'Average coodinate policy';
 279 is $f->end, 90;
 280 is $f->length, 41;
 281 is $f->to_FTstring, '(50.60)..(80.90)';
 282 isa_ok($f->coordinate_policy, 'Bio::Location::AvWithinCoordPolicy');
 283
 284 # to complete the circle
 285 $f->coordinate_policy(Bio::Location::WidestCoordPolicy->new());
 286 is $f->start, 40, 'Widest coodinate policy';
 287 is $f->end, 100;
 288 is $f->length, 61;
 289 is $f->to_FTstring, '(40.60)..(80.100)';
 290 isa_ok($f->coordinate_policy, 'Bio::Location::WidestCoordPolicy');